Exploration of structural requirements for the inhibition of VEGFR-2 tyrosine kinase: Binding site analysis of type II, ‘DFG-out’ inhibitors

Abstract

The conserved three-dimensional structure of receptor tyrosine kinases (RTKs) has been varyingly observed in prokaryotes to humans that actively participate in the phosphorylation process of tyrosine residues in the protein, which results in the alteration of protein’s function. Mutation and transcriptional or post-translational modifications lead to a deregulation of kinases, which ultimately fallout into the development of pathological conditions like cancer. The human genome encodes two kinds of tyrosine kinases: non-receptor tyrosine kinases (NRTKs) and receptor tyrosine kinases (RTKs). Among these kinases, VEGF/VEGFR-2 signaling cascade is an important target to develop novel small-molecule inhibitors for the therapy of abnormal angiogenesis incorporated with cancer. Due to advances in the knowledge of the catalytic domain and ‘DFG-motif’ region, selective ‘DFG-in’ (type I) and ‘DFG-out’ (type II) VEGFR-2/KDR inhibitors were successfully developed, and some are in different phases of a clinical trial. ‘DFG-out’ (inactive) confirmation has significant advantages over ‘DFG-in’ (active) confirmation concerning the affinity of the ATP at the catalytic domain. Further, in the catalytic domain, between front and back cleft, smaller gatekeeper residue (Val916) present; therefore, selectivity against VEGFR-2 could be precisely achieved. In this review, small molecule type II/‘DFG-out’ inhibitors, their conformation, interaction at receptor binding pocket, and structural requirements to inhibit VEGFR-2 at the molecular level are discussed.

Highlights

• VEGFR-2 is a type of membrane-bound receptor tyrosine kinases (RTKs) that regulates the process of vasculogenesis and angiogenesis.

• Small molecule first-generation type I, ‘DFG-in’ and second-generation type II, ‘DFG-out’ VEGFR-2 inhibitors exhibit clinical benefits in the treatment of aberrant angiogenesis associated with cancer.

• Molecular docking of FDA approved and novel type II inhibitors were performed using X-ray crystal structures of VEGFR-2; binding site analysis was carried out.

• Structural requirements for the inhibition of VEGFR-2 were identified.

Graphical Abstract

Communicated by Ramaswamy H. Sarma

Keywords:

• VEGFR-2
• Angiogenesis
• ‘DFG-in’
• ‘DFG-out’
• Docking
• Inhibitors

Acknowledgements

The authors are grateful to Dr. Shivajirao Kadam, Chancellor, Bharati Vidyapeeth (Deemed to be University), Pune, and Dr. Kakasaheb R. Mahadik, Principal, Poona College of Pharmacy, Pune, Maharashtra, India, for their encouragement.

Author contributions

Both the authors, Siddharth J. Modi and Vithal M. Kulkarni, have approved the final version of the manuscript and contributed equally.

Disclosure statement

The authors declare no conflict of interest pertaining to this manuscript.